[gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.

kevin kevin.len at foxmail.com
Wed May 16 04:28:32 CEST 2012

Hi, everyone.
 It is my first use of Gromacs and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is expressed in form of expectation(or moment of n-th order). This is unlike the common 'micro' constraint(simply function in terms of variable in SDE) . I can not find such a subrountine for solving constrained SDE in MD codes in Gromacs.  I see there is an algorithm called "SHAKE" or "RATTLE "which and it seems they could implement Langevin(or Brownian) dynamics with constraints. If convenient, could anyone help to point out which subroutine is specific for implementing SHAKE/RATTLE? Thanks in advance.

 Kevin Len
 Department of Materials Science
 Fudan University
 220 Handan Road Shanghai, CHINA, 200433
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120516/45cbb79f/attachment.html>

More information about the gromacs.org_gmx-users mailing list